The Parisian club has now claimed the season-opening trophy on 14 separate occasions.
Paris Saint-Germain required a dramatic equaliser followed by a successful spot-kick decider to overcome their arch-rivals in the Gulf and secure a fourth straight French Super Cup title.
The Champions League holders seemed to be sailing towards a straightforward win in the showdown between the Ligue 1 winners and the Coupe de France holders after the French winger found the net early on.
However, Marseille fired twice late to take a shock advantage. Initially, the English forward scored from the spot-kick, before Willian Pacho unfortunately turned the ball into his own net for an own-goal.
In a remarkable turn of fortune, the Portuguese striker snatched a vital equaliser in the final moments to force the match into a penalty shootout. PSG goalkeeper Chevalier then stood as the hero, saving crucial attempts from Matt O'Riley and Traore.
In the shootout, Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted successfully for Paris Saint-Germain to complete a 4-1 shootout victory.
Now 14-time winners Paris Saint-Germain, who met last season's Ligue 1 second-placed team Olympique de Marseille after completing a league and cup double, have now won this competition for the twelfth time in the last thirteen seasons.
